Gavin Melaugh wrote:
Thanks Justin
Is it possible to use g_wham with pull_geometry = direction, I read on
the website that you couldn't but was wondering if this had changed?
Nothing has changed as far as I am aware. Also keep in mind the difference
between SMD and umbrella sampling. They are separate procedures, as hopefully
my tutorial has made clear.
-Justin
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Hi All
I am using COM pulling to pull two molecules together in order to
calculate the potential of mean force and the pulling is fine. I am
using pull = umbrella for the pulling as I am following
the tutorial on the website. If I use pull = constraint does this still
pull the molecules together, and if so do you still then need to
perform umbrella sampling on the configurations generated? I am a little
confused as I don't understand how the molecules pull together if they
are constrained.
For plain SMD, you can use any of the pull methods. In the tutorial I
wrote, I explain why I used "pull = umbrella" during SMD. Umbrella
sampling is a separate procedure, which can be done after SMD. If you
want a free energy along the reaction coordinate, there are several
methods for doing this, among which is umbrella sampling.
-Justin
Many Thanks
Gavin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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